Man pages for jjellis/GenomicVis
Genomic Visualisation Routines

CNVDataAn example of a CNV data frame used by 'cnv.heatmap'.
CNVExampleAn example of a CNV data frame used by 'cnv.plot'.
cnv.heatmapCreate a CNV heatmap.
cnv.mergeMerge CNVs
cnv.plotCreate a copy number and structural variant plot.
default.cnv.heatmap.colour.mapCNV heatmap colour scheme.
filter.breakdancerIllustrative funtion to filter Breakdancer calls.
gap2cnvIllustrative function for processing GAP data.
genes.in.regionFind gene in a genomic interval
GenomicVisGenomic Visualisation
hg19GenesA 'GRanges' instance that contains hg19 gene locations taken...
kataegisCalculate regions of kataegis from a VCF file.
kataegis.coloursDefault colours for kataegis plot.
KataegisExampleAn example of output from the 'kataegis' function.
list.vcffilesList VCF files in a directory.
plotKataegisPlot a kataegis rainfall figure.
plot.kataegisListCreate a kataegis "rainfall" plot.
prepare.dataPrepare data for plotting.
print.kataegisListPrint function for kataegisList
read.breakdancerIllustrative function to read the output of Breakdancer.
read.gapIllustrative function to read GAP output.
read.illuminaIllustrative function to an Illumina GenomeStudio file.
read.snpeff.vcfRead a SnpEff annotated VCF file.
read.snpeff.vcfsIllustrative function to read multiple VCFs
read.vcfRead VCF
SNPExampleAn example of a SNP data frame used by 'cnv.plot'.
snv.clusteringCluster samples based on SNVs.
snv.heatmapPlot a SNV heatmap.
summarise.mutationsSummarise the types of mutations in a region of kataegis.
SVExampleAn example of a structural variant data frame used by...
vcf.vennCreate a venn diagram of SNV overlap in a group of VCF files.
jjellis/GenomicVis documentation built on May 19, 2019, 11:39 a.m.